ASaiM: A Galaxy-based framework to analyze microbiota data

Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable

In vitro susceptibility of Aspergillus spp. clinical isolates to albendazole

International audienceThe in vitro antifungal activity of albendazole, a benzimidazole widely used as an antihelmintic drug in humans, was investigated and assessed for its activity against Aspergillus spp. Forty-eight isolates, representing the most frequent species found in human pathology [Aspergillus fumigatus (n = 27), Aspergillus flavus (n = 10), Aspergillus terreus (n = 7), Aspergillus nidulans (n = 3) and Aspergillus niger (n = 1)], and one quality control strain (A. niger ATCC 9804 83435) were tested according to the NCCLS M38-P methodology for moulds. All the strains were susceptible to albendazole, with homogeneous MICs for each species; three strains were resistant to itraconazole

Fecal microbiota variation across the lifespan of the healthy laboratory rat.

Laboratory rats are commonly used in life science research as a model for human biology and disease, but the composition and development of their gut microbiota during life is poorly understood. We determined the fecal microbiota composition of healthy Sprague Dawley laboratory rats from 3 weeks to 2 y of age, kept under controlled environmental and dietary conditions. Additionally, we determined fecal short-chain fatty acid profiles, and we compared the rat fecal microbiota with that of mice and humans. Gut microbiota and to a lesser extent SCFAs profiles separated rats into 3 different clusters according to age: before weaning, first year of life (12- to 26-week-old animals) and second year of life (52- to 104-week-old). A core of 46 bacterial species was present in all rats but its members' relative abundance progressively decreased with age. This was accompanied by an increase of microbiota α-diversity, likely due to the acquisition of environmental microorganisms during the lifespan. Contrastingly, the functional profile of the microbiota across animal species became more similar upon aging. Lastly, the microbiota of rats and mice were most similar to each other but at the same time the microbiota profile of rats was more similar to that of humans than was the microbiota profile of mice. These data offer an explanation as to why germ-free rats are more efficient recipients and retainers of human microbiota than mice. Furthermore, experimental design should take into account dynamic changes in the microbiota of model animals considering that their changing gut microbiota interacts with their physiology.NG received a PhD scholar grant from the French “Ministère de l'Enseignement et de la Recherche”. WT received a PhD scholar grant from the Auvergne council. PPC received a post-doctoral fellowship from “Université d'Auvergne”. Work in PWOT's laboratory was supported by Science Foundation Ireland through a Centre award to the APC Microbiome Institute (SFI/12/RC/2273)

Les lipides polaires laitiers diminuent les facteurs lipidiques du risque cardiovasculaire chez des femmes ménopausées

Introduction et but de l’étudeDes perturbations du métabolisme lipidique à jeun et en phase postprandiale constituent des facteurs de risque cardiovasculaire. La nutrition joue un rôle majeur dans leur modulation, notamment chez les femmes ménopausées qui constituent une population à risque. Un intérêt s’est récemment développé sur les effets bénéfiques potentiels des lipides polaires (LP) laitiers, qui sont riches en sphingomyéline. A ce jour, leurs effets chez l’Homme restent cependant à clarifier, car les rares études cliniques ont jusqu’à présent été réalisées chez des sujets sains et par supplémentation, augmentant ainsi l’apport énergétique. Nous avons donc testé l’hypothèse qu’un enrichissement isolipidique de l’alimentation avec des LP laitiers apportés par un produit laitier réaliste pourrait améliorer le profil cardiovasculaire de femmes ménopausées à risque.Matériel et méthodesUn essai clinique contrôlé aléatoire en double aveugle chez 58 femmes ménopausées en surpoids a été réalisé. Les volontaires ont été soumises à (i) 4 semaines d’intervention avec consommation quotidienne d’un fromage à tartiner contenant 12g de matière grasse laitière incluant aléatoirement soit 0g (contrôle, n=19), 3g (n=19) ou 5g (n=20) de LP laitiers, et (ii) des tests d’exploration métabolique sur 8h, avant et après intervention (2 visites). Des marqueurs lipidiques ont été mesurés dans le sérum et dans la fraction riche en chylomicrons. L’effet de la dose de LP laitiers a été testé par un modèle linéaire mixte (SAS®) recherchant les différences entre visites et entre groupes d’intervention.Résultats et analyse statistiqueLa consommation du fromage à 5g-LP diminue les concentrations sériques à jeun et postprandiales du cholestérol total (−0,33±0,03mM, p<0,01) et des triglycérides (TG, −0,35±0,05mM, p<0,01), diminue le cholestérol LDL à jeun (−0,34±0,08mM, p<0,01), augmente le cholestérol HDL (+0,06±0,03mM, p<0,05) et diminue le rapport ApoB/ApoA1 (−0,07±0,01, p<0,01). Les effets sont différents de ceux du fromage contrôle (p<0,05) qui n’induit pas de modification du profil lipidique. La dose de LP laitiers modifie le cholestérol et les TG des chylomicrons (p<0,01) avec des concentrations diminuées dans le groupe 5g-LP (−0,07±0,02mM et −0,26±0,09mM, respectivement ; p<0,01), suggérant une moindre absorption intestinale et/ou une augmentation de l’épuration des résidus de chylomicrons.ConclusionCes résultats suggèrent qu’une stratégie nutritionnelle ciblée sur la qualité des lipides laitiers, incluant les lipides polaires, pourrait contribuer à améliorer la santé cardiométabolique des femmes ménopausées

Milk polar lipids reduce cardiometabolic risk factors in post-menopausal women: a randomized double-blind controlled trial

Disturbances of fasting and postprandial lipid profiles are major cardiovascular (CV) risk factors. Nutrition plays a key role in their modulation, notably in postmenopausal women at CV risk. Interest has grown on the potential benefits of milk polar lipids (MPL). However, effects of MPL supplementation in humans have been inconsistent, often due to trials being performed in healthy subjects by increasing lipid intake. We hypothesized that isolipidic enrichment of the diet with MPL via a realistic dairy product could improve lipid markers of CV risk. We notably targeted a 5-g/day dose using an originally designed butterserum microfiltration process (Gassi et al., Int. Dairy J., 2016). We performed a double-blind randomized controlled trial in 58 postmenopausal overweight women with HDL-cholesterol<1.5 mM. They were subjected to (i) a 4-week dietary intervention with daily consumption of a cream-cheese containing 12 g of milkfat randomly including either 0 g (control, n=19), 3 g (n=19) or 5 g (n=20) of MPL, and to (ii) 8h-postprandial explorations after a test meal, before and after intervention (i.e. 2 visits). Lipid markers were measured in plasma and in the chylomicron fraction. The effect of MPL dose was tested through a linear mixed model (SAS®). The 5 g MPL dose decreased fasting and postprandial total cholesterol (-0.33±0.03 mM, p<0.001) and plasma triglycerides (-0.35±0.05 mM, p<0.001), and decreased fasting total/HDL-cholesterol and ApoB/ApoA1 ratios (p<0.001) (effects different from control, p<0.05). The 5 g MPL dose decreased both chylomicron- cholesterol and -triglycerides (p<0.01), suggesting lower intestinal absorption and/or increased clearance. A pilot mechanistic study in ileostomized patients consuming the test cheeses including 2H-cholesterol tracer showed that MPL lowered intestinal cholesterol absorption. Altogether, our data suggest that a dietary strategy based on milk lipid quality, including MPL, can contribute to improve the cardiometabolic health of postmenopausal women